Ion mobility TOF/MALDI/MS using drift cell alternating high and low electrical field regions

ABSTRACT

Improved ion focusing for an ion mobility drift cell allows for improved throughput for subsequent detection such as mass detection. Improved focusing is realized by the use of alternating regions of high and low electric fields in the ion mobility drift cell.

CROSS-REFERENCE TO RELATED APPLICATION

This application claims priority to U.S. Application Ser. No.60/512,825, filed on Oct. 20, 2003.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This work has been funded in whole or in part with Federal funds fromthe National Institute on Drug Abuse, National Institutes of Health,Department of Health & Human Services under Contract No. N44DA-3-7727.The United States government may have certain rights in the invention.

TECHNICAL FIELD

The present invention relates generally to instrumentation andmethodology for characterization of chemical samples based on improvedion mobility spectrometry (IMS). Specifically, the improvements lie inthe area of ion focusing. The improved focusing may be used to improvethroughput from an IMS instrument to a downstream instrument and method,preferably mass spectrometry (MS). The resulting instrument and methodare useful for qualitative and/or quantitative chemical and biologicalanalysis.

BACKGROUND OF THE INVENTION

An ion mobility spectrometer is typically composed of an ionizationsource, a drift cell, and an ion detector; examples of the latterinclude a sampling plate, an electron multiplier, or a massspectrometer. Ion mobility spectrometry separates ions in terms of theirmobility with reference to a drift/buffer gas measuring the equilibriumvelocity which ions obtain. When gaseous ions in the presence of a driftgas experience a constant electric field, they accelerate until acollision occurs with a neutral molecule. This acceleration andcollision sequence is repeated continuously. Over time, this scenarioaverages out over the macroscopic dimensions of the drift tube to aconstant ion velocity based upon ion size, charge and drift gaspressure. The ratio of the velocity of a given ion to the magnitude ofthe electric field experienced by it is the ion mobility. In otherwords, the ion drift velocity (V_(d)) is proportional to the electricfield strength (E) where the ion mobility K=V_(d)/E is a function of theion volume/charge ratio. Thus IMS is a technique similar to massspectrometry, having a separation component to it. IMS is generallycharacterized as having high sensitivity with moderate separation power.Separation efficiency is compromised when “bands” of the various ionsspread apart as opposed to remaining together in a tight, well-definedplug. Thus, the quality of the electric field maintained in the driftcell is critical to preserving and perhaps improving separationefficiency; i.e., resolution. It is also critical in applications wherea downstream detection method is limited by ion throughput from the ionmobility drift cell. Improved focusing improves ion throughput to thedownstream instrumental detection platform, thereby improving overallperformance.

Prior art instruments employ various methods to obtain a linear electricfield including utilizing: 1) a series of equally spaced rings connectedthrough a resistor chain, 2) a tube coated with a resistive material inU.S. Pat. No. 4,390,784 to Browning et al., or 3) by a more complexmethod such as a printed circuit board assembly drift tube in U.S. Pat.No. 6,051,832 and PCT WO 98/08087 to Bradshaw. Von Helden (G. VonHelden, T Wyttenbach, M. T. Bowers Science 267 (1995) p1483) showedtransport of MALDI ions desorbed from a surface and transported into a 1Torr mobility cell and In 1995 Bristow showed the use of a MALDI matrixsurface to generate ions inside an atmospheric ion mobility spectrometer(A. W. T. Bristow, C. S. Creaser, J. W. Stygall “Matrix Assisted LaserDesorption Ionisation-Ion Mobility Spectrometry, Abstract to FourthInternational Workshop on Ion Mobility Spectrometry,” Cambridge U.K.Aug. 6^(th)-9^(th) 1995).

The combination of an ion mobility spectrometer (IMS) with a massspectrometer (MS) is well known in the art. In 1961, Barnes et al. wereamong the first to combine these two separation methods. Suchinstruments allow for separation and analysis of ions according to boththeir mobility and their mass, which is often referred to as twodimensional separation or two dimensional analysis. Young et al.realized that a time-of-flight mass spectrometer (TOFMS) is the mostpreferred mass spectrometer type to be used in such a combinationbecause its ability to detect simultaneously and very rapidly (e.g. witha high scan rate) all masses emerging from the mobility spectrometer.Their combination of a mobility spectrometer with a TOFMS, in thefollowing referred to as a Mobility-TOFMS. This prior art instrumentcomprised means for ion generation, a mobility drift cell, a TOFMS, anda small orifice for ion transmission from the mobility cell to theTOFMS.

Use of MS as a detector allows for resolution based on mass-to-chargeratio after separation based upon ion mobility. Shoff and Hardenpioneered the use of Mobility-MS in a mode similar to tandem massspectrometry (MS/MS). In this mode, the mobility spectrometer is used toisolate a parent ion and the mass spectrometer is used for the analysisof fragment ions (also called daughter ions) which are produced byfragmentation of the parent ions. In the following this specifictechnique of operating a Mobility-MS is referred to as Mobility-MS, oras Mobility/TOF if the mass spectrometer is a TOFMS-type instrument.Other prior art instruments and methods using sequential IMS/MS analysishave been described (see, e.g., McKnight, et al. Phys. Rev., 1967, 164,62; Young, et al., J. Chem. Phys., 1970, 53, 4295; U.S. Pat. Nos.5,905,258 and 6,323,482 of Clemmer et al.; PCT WO 00/08456 ofGuevremont) but none combine the instrumental improvements disclosedpresently. When coupled with the soft ionization techniques and thesensitivity improvements realizable through use of the drift cellsystems herein disclosed, the IMS/MS systems and the correspondinganalytical methods of the present invention offer analytical advantages:over the prior art, particularly for the analysis of macromolecularspecies, such as biomolecules.

The challenging issue when building a Mobility-MS is achieving a highion transmission from the mobility region into the MS region of thetandem instrument. It is at this interface that the earlier goals of ionmobility technology of using a linear field appear incongruous with thegoal of maximizing ion throughput across the IMS/MS interface. Themobility section is operating at a pressure of typically between 1 mTorrand 1000 Torr whereas the MS is typically operating at pressures bellow10⁻⁴ Torr. In order to maintain this differential pressure it isnecessary to restrict the cross section of the opening that permits theions to transfer from the mobility section to the MS section. Typicallythis opening cross section is well below 1 mm². Hence it is desirable tofocus the ions into a narrow spatial distribution before thistransmission occurs.

As discussed above, in the early development of IMS, it was believedthat the use of focusing methods (i.e., non-linear fields) wasdetrimental because it was believed that such focusing methods woulddeteriorate the resolution of the mobility spectrometer. Also, many ofthe early mobility spectrometers were used to investigate the mobilityconstant of ions, in which case it is preferable to use a homogeneousfield of known value along the ion drift path. Therefore, mostinstruments simply used a large area ion detector at the end of themobility drift and ion focusing was not an overarching concern. It wasonly when the need for compact and sensitive IMS emerged when thefocusing of the drift ions was addressed.

In U.S. Pat. No. 4,855,595, Blanchard taught a focusing method based ontime-varying electric fields. In 1992, Avida et al. U.S. Pat. No.5,235,182 found that a slight inhomogeneous fringe fields along themobility drift cell could be used to reduce the loss of ions from theedge of the mobility drift cell and hence to reduce the size of mobilityinstruments. The inhomogeneous fringe fields were generated by simplyincreasing the thickness of the field-generating ring electrodes suchthat the ratio of electrode thickness to inter-electrode gap could bemanipulated to provide the fringe fields. The following year, Thekkadath(U.S. Pat. No. 5,189,301) taught a cup shaped electrode to generate afocusing field. This field configuration compares to the Vehneltcylinder used in non-collisional ion optics. In 1996 Gillig et al.published a magnetic field to confine the ions in a small beam in orderto increase the ion transmission from the mobility section into a massspectrometer.

In 1999 Gillig used a periodic configuration of focusing and defocusingfields in order to increase the ion transmission from the mobilitysection into the MS section, as discussed above. This fieldconfiguration compares to a technique used in non-collisional ion opticswhere series of focusing and defocusing lenses are used to confine ionbeams in large ion accelerators [Septier, p. 360]. Published U.S.application Nos. 2001/0032930 to Gillig et al. and 2001/0032929 toFuhrer et al. taught the use of a specific mobility cell electrodeconfiguration to produce periodic and periodic/hyperbolic fields,respectively and superior focusing. U.S. Pat. No. 6,040,575 toWhitehouse et al., teaches surface charging of insulators to collect andslow down or selectively fragment the ions in the region of theorthogonal time-of-flight mass section.

Nonlinear electric fields have also been introduced to ion mobilitydrift cells to focus ions to a detector as presented in U.S. Pat. No.5,189,301 to Thekkadath utilizing a cup electrode and U.S. Pat. No.4,855,595 to Blanchard using nonlinear fields for the purpose ofcontrolling ions, trapping ions in a potential well to normalize driftdifferences and increase sensitivity. All of these methods havedrawbacks associated with their construction and ease of implementation.Therefore, it is the object of this invention to reduce or eliminatedisadvantages and problems associated with prior art ion mobilityinstruments.

Copending U.S. application Ser. No. 09/798,030 to Fuhrer et al., filedFeb. 28, 2001 demonstrates that additional ion focusing in IMS isachieved by using a superposition of hyperbolic and periodic electricfields in a mobility cell.

Brittain, et al., in U.S. Pat. No. 5,633,497, describe the coating ofthe interior surfaces of an ion trap or ionization chamber with aninert, inorganic non-metallic insulator or semiconductor material forthe passivation of such surfaces so as to minimize absorption,degradation or decomposition of a sample in contact with the surface.

Andrien, et al., in U.S. Pat. No. 6,600,155, describe the coating of asurface in the time-of-flight pulsing region with a dielectric filmbetween other films, suggesting an improvement of ion beam propertiesbefore orthogonal extraction of ions into the drift region of atime-of-flight mass spectrometer.

Loboda, in U.S. Pat. No. 6,630,662 describes a method of enhancingperformance of mobility separation of ions by balancing the ion driftmotions accomplished by the influence of DC electric field andcounter-flow of the gas. Using this balance of forces, ions are firstaccumulated inside the ion guide, preferably RF-ion guide, and then bychanging of electric field or gas flow, gradually elute from the ionguide to some detector, preferably a TOF MS.

U.S. Pat. No. 6,707,037 to Whitehouse describes the proposed extractionof ions of both signs from a MALDI target directly located insidegas-filled RF-multi-pole ion guide with a concentration of ions alongthe separation axis and directing them in opposite directions underinfluence of axial electric field for further mass-analysis.

All of the U.S. patents, patent applications, publications referencedherein are incorporated by reference as though fully described herein.

Although much of the prior art resulted in improvements in focusing andtherefore in ion throughput from the mobility cell to the massspectrometer in tandem instruments, there is room for additionalimprovement in ion throughput. The inventors describe herein a mobilitycell design which results in alternating regions of high and lowelectric field to provide improved ion focusing.

BRIEF SUMMARY OF THE INVENTION

The present invention makes clear the reason for focusing effect of suchtype of fields and enhances it, namely, by applying alternating high andlow electric fields, and implements other advantages of this approachproviding better mobility resolution and relatively simpleimplementation of collisionally-induced fragmentation of selected ions.The other suggestion mention in this, patent is using of micro-channelplates for inserting of ions from mobility cell with relatively high gaspressure into low pressure region of mass-spectrometer. Such an approachcan result in significant ion losses. To improve ion transmissionthrough such micro-channel plates the faces and/or the interior surfacesof the microchannels are coated by thin dielectric film and variousmeans of charging of this film by ions of the same sign as the desiredanalyte ions are herein now. A mulitpole radio frequency (RF) focusingand beam forming optic is proposed to create and transport ions emergingfrom a multichannel ion mobility cell wherein multiple ion sources aresimultaneously or sequentially injected each into its own individualchannel. The action of the RF multipole optic is to maintain thephysical separation of the individual mobility separated ions from eachmultichannel and to create and maintain a substantially parallel arrayof beamlets (which are themselves substantially parallel trajectories ofions emerging from each mobility channel) between the exit of themobility cell- and the entrance to the extractor region of a TOFMS. TheRF focusing and transport optic may be located before or after adifferentially pumped gas skimmer region or may have gas skimmer regionsincorporated into its optical design.

A number of embodiments are described herein. It should be clear thatother combinations of embodiments not expressly recited herein, butknown to one of skill in the art upon a reading of this description, arewithin the scope of the present invention.

The present invention is directed to a system and method relating to ionmobility drift cells transporting ions in a gas at high pressures. Ionsentering such a drift cell travel to the end of the cell under theeffect of an electrical field. Differences in molecular shape allowseparation of ions according to their ion mobility drift time. This cellcan also be applied as a pre-separation stage prior to a time-of-flightmass spectrometer (TOF) for the analysis of complex mixtures of chemicaland/or biological substances. This cell allows for cooling the enteringions and transmitting a large fraction of them. Ion losses throughdecomposition or discharging of electrodes are limited by using specialgeometry of electrodes and alternating strong and weak field regionswithin the cell. The application of high field is carefully applied overa distance which is less than the mean free path of the gas within theion mobility cell. This principle allows the application of severalhundred volts/mm before gas discharge occurs. Such high voltages can beused to continually refocus the ions as they periodically pass throughthe strong field regions. High mobility resolution is neverthelessmaintained because the ion trajectories are always randomized after eachrefocusing so that the distance traveled by each ion over the dimensionsof the mobility cell averages to nearly the same distance. Also, theapplication of higher voltage between selected electrodes in the cellcan provide spatially localized collision induced dissociation of ionsand their fragments for the efficient structural identification(sequencing) of complex biological analytes. When higher voltages aredesirably applied to intentionally create a discharge, the dischargedose not propagate along the length of the cell because it is nicelylocalized by the low field regions on either side.

In one aspect of the present invention there is an apparatus comprisingan ion source, a first ion mobility drift cell, said first ion mobilitydrift cell having an entrance fluidly coupled to the ion source, saidfirst ion mobility drift cell comprising at least two electrode pairshaving an intra-electrode gap between individual electrodes of a pairwhich is smaller than an inter-electrode gap between electrode pairs,and an exit. In one embodiment, the electrodes near the exit of the ionmobility cell have greater thickness than electrodes further removedfrom the exit of the ion mobility cell. In one embodiment, theelectrodes near the exit of the ion mobility cell are of smallerdiameter than electrodes further removed from the exit of the ionmobility cell. In one embodiment of the apparatus, the electrodes nearthe exit of the ion mobility drift cell have an aperture comparable indimension to the dimensions of the exit. In one embodiment, one or moreelectrode pairs near the entrance of the ion mobility cell have smalleroutside diameter than one or more electrode pairs farther away from theentrance. In one embodiment, the first several sets of electrodes nearthe entrance of the ion mobility cell have an increasing outsidediameter. In one embodiment, the apparatus further comprising an RF(radio frequency) voltage and a dc (direct current) electrode voltage,wherein said RF voltage is superimposed on said dc electrode voltage. Inone embodiment, the apparatus further comprises a time-of-flight massspectrometer fluidly coupled to the exit of the mobility drift cell byway of an orthogonal extractor and a low energy monochromatized electronbeam coupled to said orthogonal extractor. In one embodiment of theapparatus, the exit comprises a plurality of apertures. In oneembodiment, the plurality of apertures is comprised of a 4033 circulararray of apertures, the array having a diameter of 5.37 mm and a totalaperture area of 8 mm². In one embodiment, one or more electrodes in thedrift cell has a plurality of apertures. In one embodiment, thedistribution of apertures in the electrode pairs changes from theentrance to the exit. In one embodiment, the distribution of apertureschanges from a circular distribution to a horizontal rectangledistribution. In one embodiment, the exit is at least partially coatedwith a thin insulating film. In one embodiment, the insulating filmcomprises piezoelectric film. In one embodiment, the apparatus furthercomprises structures comprising piezoelectric thin films at one or morelocations within the mobility drift cell. In one embodiment, the firstmobility drift cell one or more collision induced dissociation regionswithin it. In one embodiment, the collision induced dissociation regionis placed near the exit of the mobility drift cell. In one embodiment,the collision induced dissociation region is placed near the center ofthe mobility drift cell. In one embodiment, the ion mobility drift cellfurther comprises at least one porous semiconductor electrode. In oneembodiment, the porous semiconductor electrode is located directly afterthe entrance. In one embodiment, the at least one porous semiconductorelectrode is coated with a dielectric or piezoelectric thin film. In oneembodiment, the ion source is a MALDI source. In one embodiment, the ionsource is a secondary ion source. In one embodiment, one or more of theelectrode pairs are replaced with electrodes triads. In one embodiment,at least one of the electrodes is a multiaperture conical skimmerelectrode. In one embodiment, the apparatus further comprises adifferentially pumped interface fluidly coupled to said ion mobilitydrift cell; a conical skimmer fluidly coupled to said differentiallypumped interface; an extractor fluidly coupled to said conical skimmer;and, a time-of-flight mass spectrometer fluidly coupled to saidextractor. In one embodiment, the apparatus further comprises adifferentially pumped interface fluidly coupled to said ion mobilitydrift cell; a multihole skimmer fluidly coupled to said differentiallypumped interface; an extractor fluidly coupled to said multiholeskimmer; and, a time-of-flight mass spectrometer fluidly coupled to saidextractor. In one embodiment, said ion mobility drift cell forms part ofa multibore ion mobility spectrometer. In one embodiment, at least oneof said electrode pairs is comprised of flexible copper-kapton-coppermaterial. In one embodiment, the apparatus further comprises amultichannel RF interface fluidly coupled to said drift cell; anextractor fluidly coupled to said multichannel RF interface; and atime-of flight mass spectrometer fluidly coupled to said extractor. Inone embodiment, the apparatus further comprises an second ion mobilitydrift cell fluidly coupled to said first ion mobility drift cell, saidsecond ion mobility drift cell comprising electrode pairs having anintra-electrode, gap which is smaller than an inter-electrode gapbetween electrode pairs; and, a differentially pumped interface fluidlycoupled to said second ion mobility drift cell. In another embodiment,the apparatus further comprises a conical skimmer fluidly coupled tosaid differentially pumped interface; an extractor fluidly coupled tosaid conical skimmer; and, a time-of-flight mass spectrometer fluidlycoupled to said extractor. In another embodiment, one or more of saidelectrode pairs of said first ion mobility drift cell, said second ionmobility drift cell, or both, are replaced with electrodes triads.

In another embodiment, there is an apparatus comprising a source of ionor neutral species, a first and second ion mobility drift cell, saidfirst and second ion mobility drift cells being substantiallyhorizontally opposed to one another and fluidly coupled to said source,wherein one or both of said ion mobility drift cells comprise at leasttwo electrode pairs having an intra-electrode gap between individualelectrodes of a pair which is smaller than an inter-electrode gapbetween electrode pairs, and, a first mass spectrometer fluidly coupledto said first ion mobility drift cell and a second mass spectrometerfluidly coupled to said second ion mobility drift cell. In anotherembodiment, the apparatus further comprises a fragmentation sourcepositioned to fragment ions and neutral species entering one or both ofsaid first and second ion mobility drift cells. In another embodiment,the first mass spectrometer, the second mass spectrometer, or both, aretime-of-flight mass spectrometers.

In another aspect of the present invention, there is a method ofanalyzing ions according to their mobility in a gas comprising a firstionization step to form ions from an analytical sample, introducing saidions into a mobility drift cell, applying regions of alternating highand low electric field along the separation axis of the drift cell, anddetecting the ions. In one embodiment, the method further comprises thestep of applying an RF voltage superimposed on a dc electrode voltagealong at least a part of said separation axis. In one embodiment, themethod further comprises the step of changing the charge of ions aftersaid step of applying. In one embodiment, the step of detectingcomprises detecting with a mass spectrometer. In one embodiment, themass spectrometer is a time-of-flight mass spectrometer. In oneembodiment, the method further comprises the step of RF focusing of saidions before said step of detecting with a time-of-flight massspectrometer. In one embodiment, the step of said first ionizationcomprises forming ions using a MALDI ion source. In one embodiment, thestep of said first ionization comprises forming ions using a secondaryion source. In one embodiment, the step of said first ionizationcomprises forming ions using a electrospray ionization combined with anion trap. In one embodiment, the method further comprises a secondionization step. In one embodiment, the step of applying regions ofalternating high and low electric field comprises applying twosubstantially horizontally opposed regions of alternating high and lowelectric field through the use of two substantially horizontally opposedion mobility drift cells. In one embodiment, the step of detectingcomprises detecting with a mass spectrometer. In one embodiment, thesaid step of detecting with a mass spectrometer comprises detecting witha time-of-flight mass spectrometer.

The foregoing has outlined rather broadly the features and technicaladvantages of the present invention in order that the detaileddescription of the invention that follows may be better understood.Additional features and advantages of the invention will be describedhereinafter which form the subject of the claims of the invention. Itshould be appreciated that the conception and specific embodimentdisclosed may be readily utilized as a basis for modifying or designingother structures for carrying out the same purposes of the presentinvention. It should also be realized that such equivalent constructionsdo not depart from the invention as set forth in the appended claims.The novel features which are believed to be characteristic of theinvention, both as to its organization and method of operation, togetherwith further objects and advantages will be better understood from thefollowing description when considered in connection with theaccompanying figures. It is to be expressly understood, however, thateach of the figures is provided for the purpose of illustration anddescription only and is not intended as a definition of the limits ofthe present invention.

BRIEF DESCRIPTION OF THE DRAWINGS

For a more complete understanding of the present invention, reference isnow made to the following descriptions taken in conjunction with theaccompanying drawing, in which:

FIG. 1. Schematic of an ion mobility drift cell with alternating highand low electrical field regions.

FIG. 2. Illustration of field lines in a short typical cell with threeelectrode pairs simulated by SIMION.

FIG. 3. Schematic illustration of exemplary electrode configurations atthe end of the mobility cell, 3A: thicker electrodes near the cell exit;3B: electrodes of decreasing opening diameter; 3C: electrodes with verynarrow gap and small opening; 3D: electrode doublet produced by bondingmetal discs to ceramic and laser cutting aligned holes; 3E: circularaperture.

FIG. 4. Comparison of a single-hole aperture and multi-hole aperture;4A: single aperture; 4B: cross sectional view of 4A; 4C multi-aperture;4D cross sectional view of 4C.

FIG. 5. Schematic illustration of a circular array of 50 μm diameterholes spaced by 25 μm.

FIG. 6. SIMION simulations showing the focusing effect of the multi-holeaperture, 6A; and the resulting equipotential electric field lines, 6B.6C shows a cross-section of the SIMION simulation of the configurationwhich has an addition of a third biasable element made up ofelectrically connected small cones.

FIG. 7. Schematics showing progressive change of the distribution of theholes to change the beam profile from a circular spot to a narrowhorizontal rectangle; 7A, front view; 7B, cross-sectional view.

FIG. 8. Schematic showing reduction of the ion beam size from 8 mm² openarea multi-hole aperture (corresponding to the usual {fraction (1/8)}inch diameter-opening) to the 0.07 mm² multi hole-aperture(corresponding to the usual 300 μm diameter-opening); 8A, front view;8B, cross-sectional view.

FIG. 9. Induction of a surface dipole on a highly polarizable materialusing a conical (left) or flat film-coated orifice.

FIG. 10. Two-dimensional representation of the mass-mobility spectrum ofa complex mixture of molecular ions (top) and corresponding instrumentalplatform (below): 10A, the fragmentation occurs at the end of themobility cell; 10B, the fragmentation is performed in the middle of themobility cell.

FIG. 11. Schematic of a mobility cell in an atmospheric interface massspectrometer.

FIG. 12. Simulation showing two types of ions (black and gray) moving ina 20-electrode, 3 cm-long cell under 1200 V and a 2 Torr He pressure.

FIG. 13. Same simulation as described in FIG. 12 at time of ion arrivalat end of drift tube; ion transmission is about 29%. This screen copy istaken when the ions have arrived.

FIG. 14. Same simulation as described in FIG. 12 with potential modifiedbetween electrodes in last three pairs; ion transmission is about 56%.

FIG. 15. Simulation showing two types of ions (black and gray) moving ina 12-electrode, 3 cm-long cell under 1200 V and a 2 torr He pressure.

FIG. 16. Same simulation as described in FIG. 15 at time of ion arrivalat end of drift tube; ion transmission is about 56%.

FIG. 17. Same cell characteristics and simulation parameters asdescribed in FIG. 16 except that a higher overall axial voltage isapplied (1800 V instead of 1200 V).

FIG. 18. Same simulation as described in FIG. 17 at time of ion arrivalat end of drift tube; ion transmission is about 71%.

FIG. 19. Same cell characteristics and simulation parameters asdescribed in FIG. 15 except that a 100 V-RF voltage is superimposed tothe DC axial voltage (1200 V).

FIG. 20. Same simulation as described in FIG. 19 at time of ion arrivalat end of drift tube; ion transmission is about 36%.

FIG. 21 Same cell electrode characteristics and configuration asdescribed in FIG. 15 monitoring the transmission of SIMS ions; iontransmission is about 42%.

FIG. 22. Same cell characteristics and simulation parameters asdescribed in FIG. 21 except for the higher beam energy (1 eV instead of0.1 eV) and field in the ionization interface (50 V/cm); Iontransmission is about 9%

FIG. 23. Schematic of mobility cell breakdown voltage and transmissiontesting setup; 23A, wide opening at the skimmer; 23B, narrow orifice andside openings.

FIG. 24. Copy of an AutoCAD drawing of the cell mechanical design.

FIG. 25. A typical 2D mass-mobility spectrum obtained using thedescribed mobility cell of FIG. 24.

FIG. 26. 26A, combination of a special mobility interface tube with thedifferential pumping including a conical skimmer; 26B, detailed view ofthe interface drift tube.

FIG. 27. Schematic of the setup for bipolar mass spectrometry of aerosolparticles. Schematic of tandem arrangement for injecting either mobilityseparated ions, mobility separated ionized particles, or neutralparticles into the ionization region between to mobility TOFMS apparatusfor separating and measuring mobility and fragmented ions or ionsdesorbed from the injected particles.

FIG. 28. 28A: Schematic view of RF interface between mobility cell andmass spectrometer; 28B: Cross-sectional view of one RF interface region.

DETAILED DESCRIPTION OF THE INVENTION

As used herein, “a” or “an” means one or more. Unless otherwiseindicated, the singular contains the plural and the plural contains thesingular.

As used herein, “aperture” means “hole” or “orifice”.

As used herein, an “electrode triad” is a distinct group or cluster ofthree electrodes.

As used herein, the term “intra-electrode gap” refers to the gap betweentwo electrodes of an electrode pair.

As used herein, the term, “inter-electrode gap” refers to the gapbetween electrode pairs.

As used herein, “MALDI” means matrix assisted laser desorptionionization.

As used herein, “SIMS” means secondary ion mass spectrometry.

As used herein, the term “TOF” is defined as a time-of-flight massspectrometer; as used herein, “oTOF” is defined as a time-of-flight massspectrometer configured orthogonally to the analytical axis of apreceding instrumental platform such as, for example, the separationaxis of an ion mobility cell.

As used herein IM-oTOFMS refers to a combination of an ion mobilityspectrometer with an orthogonal time of flight mass spectrometer.

Electrode Configurations for Ion Focusing

In applications where ion mobility cells filled with a few Torr ofbuffer gas are used as a volume/charge separation stage in front of amass spectrometer, the cooled ions exit through a small aperture into adifferentially pumped low pressure region within the mass spectrometer.To minimize transmission losses within the ion mobility cell at the exitorifice, the ion beam inside the drift cell has to be focused.

In the new design of the present invention, alternating regions of highand low field are used to provide the focusing (FIG. 1) along the entiremobility cell which is filled with gas at a pressure of between 1 andseveral hundred Torr. Most commonly this gas will be helium, althoughother gases or gas mixtures may be used. The alternating high and lowfield regions are created by varying the distance between electrodes,while the bias voltage between all electrodes is the same.Alternatively, the small gaps (7) and the large gaps (15) betweenelectrode pairs may be biased by independent power supplies to anydesired ratio limited only by the onset of electrical discharge throughthe gas along the central axis of the mobility cell. The width of thesmall gap (7) is chosen so that it is comparable or less, preferablysubstantially less, than the mean free path of electron motion in thegas at a particular operating pressure. By so doing, high voltages inthese gaps can be applied without causing an electrical discharge alongthe axis of the mobility cell. A pulsed laser or particle beam or otherionizing radiation (1) is used to desorb ions and neutrals from asurface (2) (which may be a MALDI matrix preparations) so that ions andneutrals are injected into the initial ion transport region (3). Theions may be derived from a MALDI or SIMS desorption process, amongothers. Desorbed ions then rapidly (within a few hundreds ofnanoseconds) enter the ion mobility drift cell (5). In the meantime, theneutrals which were desorbed from the surface (2) are cooled and thentransported more slowly by the mobility carrier gas flow through theinitial transport region (3). A neutral post desorption ionizationsource (4) which is most commonly an energetic photon source which maybe a laser is timed to intersect these cooled neutrals as they migrateaway from the surface (2). The post ionized neutrals will then enter themobility cell (5) some several microseconds after the directly desorbedions. High field regions are created between the sets of two veryclosely spaced electrodes rings (“paired” electrodes), one of which isillustrated by (7). Also, several of the small gaps, for example (9) and(11) can be configured so that additional voltage pulses can be appliedto achieve collision-induced dissociation of mobility separated ionswithin these gaps. These gaps are configured with at least twoelectrodes to which a momentary voltage pulse is applied sufficient toproduce a collision induced dissociation of a particular mobilityseparated ion which has just entered this region of the mobility cell.Dissociation of mobility separated ions can also be achieved byimpinging ionizing radiation (10) at a specified time during which amobility separated ion enters an intra-electrode gap (13). This ionizingradiation may be a laser which is focused through a transparent windowinto the intra-electrode gap (13). The gap (13) between individualelectrodes in an electrode pair is a high field region, while the gap(15) between electrode pairs (23) is a low field region. Fieldpenetration from the narrow gap between electrodes into the large gapprovides a component of electric field in the direction perpendicular tothe axis, which leads to the focusing of ions. Cooled ions (17) exit themobility drift cell (5) after passing the final electrode pair, i.e.,the exit pair (19). The ions then proceed to the mass spectrometerentrance (21).

An example of this field penetration for different inter-electrodespacings is shown in FIG. 2 (a SIMION simulation). The relevantparameters are as follows. The entrance field is 100 V/cm. The distancebetween the target and first electrode is 5 mm. The thickness of theelectrodes is 200 μm and the opening diameter 2.2 mm. The intra-pair gapis 1.6 mm and inter-pair gap 4 mm. 100 V is applied between eachelectrode, creating fields of 625 V/cm inside a pair and 250 V/cmbetween pairs. Field penetration can be seen in front of the entranceregion which focuses the ions toward the cell separation axis. The exitpair is also shown: the electrodes are thinner (100 μm) and only 100 μmapart. The gap between this exit pair and the precedent pair is alsosmaller (0.5 mm). 100 V is also applied between the exit and precedentpairs (200 V/cm) and inside the exit pair electrodes (10 kV/cm). Asshown by the field lines, the exit electrode pair prevents thedefocusing at its entrance. The beam is further focused to enter the lowpressure analyzer region through the 300 μm aperture. The equipotentialelectric field lines help to visualize the focusing field effect. Insidethe small gaps there is an opposite component that tends to defocusions, but the field is stronger, and, therefore, the ions move muchfaster and spend less time in this region compared to the large gaps.The net effect consists in preventing ions from being lost on theelectrodes and in their concentration close to the cell axis, andfinally, their transmission through the skimmer orifice.

Additional focusing of ions into the orifice can be achieved by aspecial configuration of a few last electrodes. In one embodiment, thethicker electrodes can be used at the end of the cell (FIG. 3A). Inanother embodiment, decreasing diameter of electrodes is used (FIG. 3B).Finally, it is possible to use a pair of electrodes with a very narrowgap and small opening comparable with the exit orifice (FIGS. 2 and 3C).The “opening” is the space between the upper and lower electrodes andshould be distinguished from both the inter- and intra-electrode gaps.Strong field penetration from this gap is likely to provide goodfocusing of the ion beam into the mass spectrometer.

A way to produce such doublet electrodes is shown in FIG. 3D. Thesedoublets can be made by bonding metal discs to ceramic and laser cuttingaligned holes in both pieces of metal. Alternatively the discs can bemade out of polyimide which is metalized on both sides. Typicaldimensions of the hole size might be 0.5 mm and the spacing of thedoublet is also 0.5 mm. FIG. 3E is a front view of the doublet electrodeof FIG. 3D. Thus, approximately three times the number of these doubletsin the same linear distance as shown in the SIMION simulation of FIG. 2could be used. It is possible to raise the voltage several times higheras compared to the more widely spaced geometry of the larger gappedstructures shown in FIGS. 1 and 2 without increasing the fragmentationof the molecular ions.

The distance between two adjacent electrodes should be smaller orcomparable to the mean free path of electrons at the cell gas pressurein order to prevent the development of the electron avalanche and theglow discharge in the high field region. The risk of starting adischarge through the channel will be eliminated since high energyelectrons formed inside the high field region are slowed down in the lowfield regions and are unlikely to propagate the discharge. Low fieldregions are created between the paired electrodes by positioning thepaired electrodes so that there is a significantly larger space betweeneach pair (inter-electrode gap) than that between the electrode elementsof each pair (intra-electrode gap).

With the alternation of low and high fields, it is possible to use amuch higher overall voltage bias along the cell without incurring gasdischarge, compared to a cell having equally spaced electrodes. Thehigher average field will result in higher average drift velocity ofions and better mobility resolving power in a shorter overall geometry.Overall ion transmission and resolution will be improved as the iontrajectories will be continuously refocused closely along the axis ofthe tube.

The use of narrower gaps in the instrument of FIG. 1 accomplishesseveral things. For example, the field strength which can be appliedwithout breakdown at higher pressures increases. The mean free path ofthe gas becomes shorter as the pressure increases and collisions becomemore frequent. Accordingly, the small gap width must be matched to beabout of the mean free path for electron-atom collision or breakdownwill occur at a lower voltage than that desired. As a result, the holesizes must also decrease so that the field penetration from the narrowgap between electrodes into the large gap (as shown in FIG. 2) can becontained to a region not much larger than the hole diameter. Thisprevents discharge, but still allows some field penetration so that theions traversing the large (low field) gap will experience a focusingfield as they approach the first electrode of the high field small gapdoublet (electrode pair).

As is also shown in FIG. 1, additional measures may be taken to prevention losses in the region between the source and the entrance of themobility cell. The first several sets of electrodes have a small butincreasing outside diameter so that it is possible to position theentrance of the cell very close to the sample (about 4 mm) and stillallow for the laser or ion beam to be incident at a steep anglenecessary to obtain good focusing. This small physical profile of themobility cell is especially useful in applications where a miniaturizedapproach to the mobility and/or mass spectrometry is required. One suchimportant example is in the case of a Laser Desorption Microscope (suchas the well-known LAMMA design) which may be substantially improved ifthe mass spectrometer minimally interferes with the coaxial axis of theSchwarzschild optics which focus the laser onto a submicron area of thesurface. The advantages of this design have been demonstrated bothexperimentally and by simulations. Additionally, an RF voltage can besuperimposed on the dc electrode voltage to enhance the ion focusing.

High Voltage Biasing of the Cell

Another advantage of these structures has to do with improving theperformance of orthogonal MALDI or electrospray mass spectral analysis.In state of the art orthogonal MALDI for example, the ions are desorbedinto several tens of mTorr pressure and cooled with quadrupoles whichare operated near electrical ground reference. The cooled ions are theninjected into the orthogonal extraction plates in an orthogonaltime-of-flight mass spectrometer (OTOF) where they are given up to a fewkilovolts of energy from the high voltage pulse applied to the extractorplates. The ions then disperse in either a linear or reflector time offlight section. They are given their final high kinetic energy by anattractive electrical potential which is applied to the front of thedetector. This potential is maintained at as high an attractiveelectrical potential as possible to give the ions maximum accelerationenergy to enable the best possible detection of large biomolecular ions.This high electrical potential requires that the output of the detectorbe either optically or electrically decoupled from the amplification andtiming circuitry which is operated at ground. This decoupling limits thehigh voltage applied to the front of the detector to around 10-20 keV orless.

In contrast, the instant mobility cell will allow the MALDI ions to beformed near ground potential and then they can climb (or descend) withinthe mobility cell to high voltages such as −10 keV before they enter themass spectrometer. The mass spectrometer must then be floated to thishigh potential; however, if the sign of the charge of the bio-ion can bechanged in the orthogonal extraction region of the time-of-flight massspectrometer (TOF) from positive to negative, the ion detector in theTOF can be operated with its output at ground. Changing the charge maybe accomplished by a low energy monochromatized electron beam tuned toelectron attachment resonances of the ion and subsequent neutral speciesafter the attachment of two electrons. This electron beam canalternatively be used to fragment the ions within the orthogonalextraction region into positive and negative fragments which can then beaccelerated into the mass spectrometer using appropriate biasing.Alternatively, the charge may be changed by chemical ionizationreactions which would change the charge from positive to negative whilethe ions are in the region between the orthogonal plates. Alternatively,the charge can be altered by photo-affinity labeling the analyte withsome negative ion adduct or electron attachment reactions. The detectordoes not have to be operated at ground potential but can be biased tobetween 10-20 keV so that the kinetic energy of the large bio-ions wouldfor example approach 30 keV upon reaching the detector. This chargeconversion in the orthogonal plates not only improves the detectionefficiency, but it also may improve specificity and reduce clutter byionizing only certain types of molecules which have electronegativegroups such as sulfhydrils or phosphate. Another well known example isthe energy specific. (resonant) attachment of electrons to smallmolecules such as explosives which contain nitro groups or largerbiomolecular ions. The ability of the instant mobility cell to withstandhigh voltages without causing gas discharge makes it easier to timevoltage sequences so that the entire electrical potential of the IMS andTOF spectrometers can be raised or lowered linearly or non-linearlyduring the time that the desorbed ions are inside the mobility cell. Inthis way the electrical potential of the ions exiting the mobility cellwill be increased relative to the electrical potential of the iondetector in the TOF. This facilitates detection larger and larger ionssuch as for example proteins.

Concept of Multi-Apertures

The use of a multi-hole aperture instead of a single-hole aperturehaving a similar total open area improves the transmission anddifferential pumping from the mobility cell to the high vacuum region ofthe mass spectrometer. FIGS. 4A-D illustrate the general concept ofusing multi-hole apertures versus a single hole aperture. FIG. 4A showsa single aperture and FIG. 4B demonstrates the cross sectional view.FIG. 4C shows a multi-aperture exit and FIG. 4D shows the correspondingcross sectional view FIG. 5 shows an example of an arrangement of holesin a circular array comprising a web area (25). Such a circular arraywill ideally have about 4033 holes and will be used to replace the{fraction (1/8)} inch diameter single-hole aperture. The same openingarea of 8 mm² will be covered by a 4033 holes-circular array of 5.37 mmdiameter. The holes are 50 μm diameter spaced by 25 μm. The {fraction(1/8)} inch diameter single hole aperture is replaced by a 4033holes-circular array of 5.37 mm diameter; both having the same openingarea of 8 mm². The 300 μm exit aperture will be replaced by an aperturewith 36 50 μm-holes distributed on an array of 508 μm diameter. Whilespecific examples in terms of dimensions have been disclosed above, itis understood by those of skill in the art that other variations in themulti-aperture embodiment are within the scope of the invention.

As shown by the SIMION simulations (FIG. 6), the field created between apair of multi-hole apertures separated by 25 μm focuses the cooled ions.As the diameter of the array of holes is larger than the single-holediameter, the array “intersects” with a larger part of the cooled ionbeam than a single hole-aperture. With the focusing effect of the holes,the transmission is enhanced. The multi-hole aperture also reduces thespace charging. Since the mean free path of the mobility gas (about 1 mmin 1 Torr He) is larger than the hole diameter, the multi-hole aperturelikely intercepts more molecules than a single-hole aperture having thesame opening area. In other words, the multi-hole aperture helpsdifferential pumping. The transmission will be significantly enhanced bythe use of a multi-hole aperture instead of single-hole aperture. Thefield penetration between holes focuses the ions. In this simulation (invacuum), the electrodes are 5 μm thick, the insulating material (e.g.polyimide) is 25 μm thick. The cooled ions have initial energy in the mVrange and are accelerated by 500 mV in front of the first multi-holeaperture. Between the two multi-hole apertures, a field of 24 V/mm isapplied. FIG. 6C shows a cross-section of the SIMION simulation whichtracks ions into a multiaperture paired exit electrode to which a thirdbiasable electrode has been added. This third electrode is situatedabove the web area (25) which is the solid electrode material andinsulator remaining on the face of the aperture between the open holes.By so positioning the biasable electrode, almost all ions approachingthis web area are deflected by the combined effects of the fieldpenetration and the gas flow into one or the several open holesbordering the specific portion of the web which the mobility ion hasapproached. It is understood also that a fourth such electrode could beadded to the back side of the multiaperture paired electrode. Theelectrodes may not need to be biasable, but could comprise a thindielectric coating which would charge to produce a dipole fieldrepulsion of the mobility ions as they approached the web area (25).Alternatively, the electrode could comprise a piezoelectric thin film(which may also be coated with a thin dielectric) which could be biasedto produce this dipole field.

The use of these multiaperture paired electrodes is not restrictedexclusively to improving the performance of the exitaperture—particularly if the third and fourth electrodes shown in FIG.6C are added to reduce or eliminate any loss of mobility ions on the webarea (25). It is then possible to use these multiaperture pairedelectrodes as the electrodes for the mobility cell region (5) itself. Ifthe size of the array is gradually reduced as the ions are transportedtoward the cell exit (keeping the size of the hole and their arrangementthe same), the focusing effect of the multiaperture paired structure canthen be used to optimize the transmission. FIG. 8 schematically showssuch a usage (the figure is not drawn to scale and shows doubletelectrodes only although it is understood that triplet and quadrupletstructures such as shown in FIG. 6C can also be used for each element).The progressive reduction of the mobility ion beam size from a 8 mm²open area multi-hole aperture (corresponding to the usual {fraction(1/8)} inch diameter-opening) to a 0.07 mm² multi hole-aperture(corresponding to the usual 300 μm diameter-opening) is schematicallyillustrated. The diameter of the circular array will be reduced from5.37 mm to 0.508 μm. The focusing effect shown in FIG. 6 and the gradualreduction of the open area will minimize the ion loss as the cooled ionsare transported from the mobility cell to the high vacuum region of theo-TOF MS. Another way to improve the transmission into the massspectrometer is to use the focusing effect of the multi-hole electrodesby gradually changing the distribution of the holes to change the beamprofile from its initial circular spot to a narrow horizontal rectangle(FIG. 7; not to scale). A gradual change of the ion beam profile fromcircular to horizontal slit-like shape produces a more focused andparallel beam in the orthogonal TOF MS extraction region. Being able tochange the mobility ion beam shape before the ions exit into high vacuum(in which case complicated octopole focusing elements would need to beused) gives many practical advantages. In addition to reducing spacecharge losses of the mobility ion beam as it is tightly focused to passthrough a single exit aperture and in addition to improving thedifferential pumping performance, this particular beam shape changeoptimizes and improves the o-TOF transmission and mass resolution. Thearrangement of the aperture holes will gradually evolve from circular torectangular and narrow. The creation of a focused and parallel beamentering the extraction, region enhances the mass resolution in theo-TOF MS.

The electrode pairs may, for example, be made from adhesivelesscopper-polyimide-copper laminates with laser-drilled holes or evenmechanically punched hole arrays.

Dielectric Coatings for Ion Focusing

The transmission of ions through an orifice such as a skimmer orifice orthe entrance of the mobility cell can be further improved by coating thearea around it with a special thin insulating film. If a certain amountof positive electrical charge (for positive ions, for negative ions thecharge would be negative) is induced on the surface of the film, themirror negative charge layer is immediately created in the conductor ata distance from the surface equal to the thickness of the film (thesurface of the conductor is a mirror surface) forming surface dipoleswith short range electrical field. The ions approaching the orifice awayform the axis are not lost in a collision with surface but are reflectedback by this field. Since the range is short, they are then attractedand reflected again. If there is a transversal component of theelectrical field near the wall, the “bouncing” ions begin to drifttowards the orifice till they reach it and go through. Thus a collectionfrom an area much wider than that of the orifice itself is achieved.

There is an optimum thickness of the insulating film that is able toretain necessary amount of charge to produce a field strong enough forions with typical energy distribution to be reflected. The density ofthe surface charge on the film is restricted by the field strengthinside the film which should be less than the breakdown limit. For usualdielectrics this limit is about a few million Volts per cm. The fieldinside the film is proportional to the charge density on the surface,inversely proportional to the permittivity of the material of the filmand does not depend on the thickness of the film. For example, chargedensity of 10¹² elementary charges per 1 cm² provides the field strengthinside the film of about 106 V/cm for a film which has a typicalpermittivity of 2. For the 0.1 μm thick film there is a 10 V potentialdifference between the surface and the conductor. In most cases this issufficient for ions moving along the surface to be reflected as iontemperature for complex ions can be only a few times larger than theroom temperature, or the “orthogonal” (to the surface) part of theirkinetic energy cannot be much larger than 0.1 eV. Otherwise ions woulddecompose very fast. For such film thickness, the electric field becomesnegligible from 1 μm away from the surface. It means that such films aresuitable for coating the walls of channels and tubes of 10 μm diameterand larger. However when large mass ions move orthogonally or close toorthogonal direction to the surface they may have more energy. In thiscase the thickness of the film should be increased proportionally to theenergy of ions of their motion in the direction orthogonal to thesurface. The charge can be induced by several methods. First, it can bea spontaneously induced by the ions of analyte/matrix impinging onto thesurface. Once critical density is achieved, the ions are reflected andthis density level is maintained automatically. In order to acceleratethis process (particularly in case of low ion fluxes) a preliminarycharging by a low intensity electrical discharge in gas can beperformed. Care should be taken in order not to damage the coating bythe discharge.

It is possible to induce a surface dipole in a highly polarizablematerial such as, for example, a piezoelectric thin film e.g. PZT (leadzirconate titanate or Pb(Zr_(x)Ti_((1-x)))O₃) film by having additionalbiasing electrodes implanted on the surface. FIG. 9 shows two possibleapproaches that involve either a flat (27) or conical (30) surface,coated with a piezoelectric thin film (33) around an orifice (42).Negative charges which initially were formed on the film surface closeto the conductor should be totally compensated by corresponding positivecharges on the conductor surface so they are not shown. A segmentedconical surface (with increasing negative voltage towards the orifice)is a preferred configuration since it provides a strong component of thefield (39) along the surface that helps to push in the direction of theorifice the ions that are randomly reflected. Incoming ions (36), bytheir reflections on the wall, are focused towards the orifice due tothe field curvature are shown. It should be obvious that this type ofstructures could be applied to any of the electrode areas within themobility cell to reduce ion loss and improve focusing within the cell asalready mentioned, for example, in FIG. 6C. This structure can also becoated with a dielectric thin film and RF voltages can also beindividually applied to the segmented electrodes.

The use of piezoelectric structures at strategic places (e.g., collisioninduced dissociation gaps 9 and 11 in FIG. 1) within the mobility cellis also a convenient way to create a gas discharge which can be used topromote a desired chemical reaction or achieve molecular ionfragmentation.

CID in the Mobility Cell

Another possibility using this type of mobility cell is also illustratedin FIGS. 10A and 10B, which demonstrate a two-dimensional representationof the mass-mobility spectrum of a complex mixture of molecular ions.Ions of different classes (e.g., peptides and lipids) form different“trend lines”. If only ions of a specific mobility drift time range(marked with dashed lines) fragment, all the fragments are aligned alonga separate trend line. In FIG. 10A, the fragmentation occurs at the endof the mobility cell; in FIG. 10B the fragmentation is performed in themiddle of the mobility cell. It is of further advantageous to use two ormore collision induced dissociation (CID) regions along the cell. InFIG. 10A, the CID gap (45) is at the end of the drift cell near the exitelectrode pair (48). Cooled ions (51) exit the cell. In FIG. 10B, theCID gap (53) is in the middle of the mobility cell. This configurationsalso has an exit electrode pair (56), with cooled ions (59) exiting thecell. All other components are as described for FIG. 1. The voltagebetween selected adjacent electrodes can be increased to a level wherehigh kinetic energy collisions start to fragment the analyte ions. Hereagain, very high voltages can be applied without inducing electricaldischarge in the carrier gas because of the mean free path length of thecarrier gas is longer than the distance between electrodes and thisrepresents considerable improvement over other such dissociation deviceswhich have been previously propose in the prior art. The dissociatingvoltages can be applied either in DC mode so that all ions going throughthe region undergo fragmentation, or by applying a short voltage pulse,or laser pulse, or glow discharge pulse so that only ions present in thegap at the time of pulse application are decomposed. If the ions havebeen previously pre-separated in time by their shapes, only ions with acertain collision cross section will be fragmented. When they aredetected by the mass analyzer, they fall onto different “trend lines” inthe two-dimensional mass-mobility spectrum (FIG. 10A), thereby improvingoverall resolution. These lines are usually formed by molecules ofsimilar shape and structure but different mass (such as peptides, orlipids).

As shown in FIG. 10A, the trend line of the fragments of the parentmolecule A is parallel to the x-axis contrary to the parent trend lines.The knowledge of the source of fragments thus can allow obtainingstructural information (sequence) of the parent ions without anyadditional MS stage.

If the fragments (as well as parent ions) are allowed to further travelthrough the remainder of the cell (for example, if the CID (53) isperformed in the middle of the cell), they are further resolved. As aresult, fragments now align along their own separate trend line (FIG.10B). If an additional (either DC or pulsed) CID stage is implemented atthe end of the mobility cell, it is possible to perform furtherselective fragmentation of these fragments. These selectivefragmentations, in effect, produce an instantaneous multiple MS setup.The feasibility of further MS^(n) stages is only limited by thenecessity of additional stages which may ultimately limit eithermobility resolution or ion transmission into the mass spectrometer.

The fact that the fragmentation occurs inside the gas filled cellguaranties the collisional cooling of the fragments. This maintains highmobility and mass resolution for both parent and daughter ions, becauseit allows forming high quality ion beams at the exit of the mobilitycell.

The vacuum enclosure of the mobility cell can be easily achieved byplacing viton O-rings between electrodes and compressing the wholestructure. Since the vacuum requirement for this section is not verystrict (the pressure is in the Torr range), little compression is enoughto maintain the purity of the mobility carrier gas. Alternatively,optically transparent glass can be used to allow introduction of photonbeams for promoting ionization or ion (or electron) molecule reactions.

Mobility Cell in an Atmospheric Interface

The small gapped electrode structure can be used to improve iontransmission from a high pressure or atmospheric pressure region into alower pressure mobility cell as shown in FIG. 11, which is across-sectional schematic of an atmospheric ion mobility massspectrometer. The key is a porous semiconductor (62) which can be usedto split the gas flow after the ion pass the entrance aperture (63)separating the ion source (83) from the mobility cell. The semiconductorcan be biased positively to repel the positive analyte ions and keepthem from following the gas flow into the pumps. The first electrode ofthe mobility cell is at high negative voltage so that the fieldpenetration up to the entrance aperture also helps to preferentiallydrag the positive ions down the axis of the mobility cell. After exitingthe drift cell (65), the ions enter a differential pumping interface(68) and mass spectrometer (71). Electrically isolated vacuum breaks(74) with pumping (77) are used throughout the instrumental platform.

Several of these porous semiconductor pumping structures (62) can beinterspersed along the length of the mobility cell. The function of anyof these structures can either be to take gas out of the cell or it canbe used to put a specific type of gas into a localized region of thecell for purposes of chemical ionization. For example, a narrow gasregion can be preferentially biased to such a high field so thatfragmentation takes place. If one of the “pumping” structures exists inthis small gap region, then it can be used to inject a gas stream whichcan chemically ionize some of the fragment ions.

Another possibility is to coat the surface of the porous structure witha piezoelectric ionizer structure which could be used to initiate a glowdischarge at will within the ion mobility cell in a specific region. Areactive gas can be injected through the porous semiconductor at thesame time into this discharge region so that the ions that are in thismobility region can be fragmented or chemically adducted.

Potential applications for this type of a drift cell comprise, but arenot limited to 1) Ion mobility drift tube in the combination IonMobility and High Pressure MALDI Mass spectrometry; 2) Ion mobilitydrift tube in the combination of Ion mobility and Secondary Ion Massspectrometry; 3) Pressure interface for the high pressure sources, suchas Electrospray Ionization and Atmospheric Pressure MALDI. Thedifference between the systems is the pressure in the region where theions are formed. For Medium Pressure MALDI, ions are generated atsimilar pressures to that of the mobility cell (a few Torr). For SIMS,ions are formed in higher vacuum (a few mTorr) and travel against theflow of the carrier gas as they enter the drift cell. When the driftcell is used as an interface, the pressure in the source region ishigher (up to 1 atm). In the latter case an additional differentialpumping of the cell is required. If the influence of the gas fluxes orthe ion diffusion can be minimized or used for the benefit of the hightransmission, the same basic design can be applied to all this varietyof applications.

Computer Simulation Results

The following computer simulations were performed for the Ion Mobilityinterfaces with Medium Pressure MALDI MS and SIMS. Different geometriesand sizes of electrodes were tried in order to optimize the transmissionand resolution of the drift cell. The total length of the mobility cellwas lower then what is used in the experimental design due to thelimited computational power, but the simulation tries to closely imitatethe geometry and the field distribution.

1. MALDI

A. 3-cm Long tube/20 Ring Electrodes

Simulations performed for the following set of parameters in a 3 cm longcell show a transmission of about 30% when applying a total axial fieldof 1200 V for two types of singly charged ions with the initial energyof 1 eV and masses of 360 and 720 a.m.u. with the same or similarcollision cross sections. Under these conditions, there is nodecomposition of ions inside the drift cell.

-   -   Helium gas pressure: 2 Torr    -   Electrode thickness: 0.1 mm    -   Distance between paired electrodes (which is close to the free        path length of electrons in 2 Torr He): 0.5 mm    -   Distance between pairs: 2 mm    -   Initial inner ring diameter: 1.6 mm    -   Inner diameter of the ring pair before the exit pair: 1 mm    -   Inner diameter of the exit pair: 0.3 mm    -   Distance between the two last rings: 0.3 mm    -   Initial beam size: 0.3 mm

The results of simulations in these conditions are shown in FIG. 12 andFIG. 13. FIG. 12 is a snapshot taken when ions travel inside the tube.The mass of the darker ions is 360 amu and they have a 116 Å²cross-section. The mass of the lighter ions is 720 amu and they have a116 Å² cross-section. The field in the ionization interface is 200 V/cm.The initial ion beam energy and diameter are 1 eV and 300 μm,respectively. The electrode thickness is 100 μm. The distance betweenpaired electrodes is 500 μm and between pairs 2 mm. The inner ringdiameter is 1.6 mm except for the pair before the exit pair (1 mm) andfor the exit pair (300 μm). This snapshot of the simulation is takenwhen the ions have already traveled through roughly ⅔ of the drift cell(after 40 μs). No ions are lost by decomposition or discharge on thering surface. The estimated resolution is then about 20. FIG. 13illustrates the end of ion travel inside the drift cell. Fifty-eightions out of initial 200 are transmitted through the orifice. The overalltransmission is about 30% and the resolution is at least 20. Ions arelost at the before-last electrode pair and the exit electrode pair. Thesimulation software, also provides the standard deviation and arrivaltime. The resolution can then be calculated knowing that for Gaussianpeaks, the full width at half maximum is a standard deviation multipliedby 2.35.

When the potential between electrodes in the last three pairs isdoubled, ion transmission greater than 50% is achieved (FIG. 14).Applying a larger axial voltage of 1800V instead of 1200 V increases theion transmission to the value of about 60%. FIG. 14 shows the same ionmotion conditions as described in FIG. 12 with modified (field in theionization interface set at 100 V/cm). The cell is slightly differentfrom the cell described in FIG. 12. The gap between paired electrodes ofthe three last pairs is gradually reduced as well as their innerdiameter. The potential difference in the last three pairs is twice thepotential difference in the other pairs. This snapshot is taken when theions have arrived. The overall transmission is about 55%. Ions are lostat the three last electrode pairs.

B. 3-cm Long Tube/12 Ring Electrodes

In a cell of the same length but with fewer and thicker electrodes, 112out of 200 initial MALDI ions pass through; this is more than 50% of iontransmission at the same He pressure and total voltage (see FIG. 15 andFIG. 16). In FIG. 15, the mass of the red ions is 360 amu and they havea 110 Å² cross-section. The mass of the lighter ions is 720 amu and theyhave a 116 Å² cross-section. The field in the ionization interface is100 V/cm. The initial ion beam energy and diameter are 1 eV and 1 mm,respectively. The detailed parameters are:

-   -   Electrode thickness: 0.6 mm except for the exit pair    -   Distance between paired electrodes: 0.8 mm    -   Distance between pairs: 4 mm.    -   Initial opening diameter: 2.2 mm.    -   Opening diameter of the ring pair before the exit pair: 1 mm    -   Opening diameter of the exit pair: 0.3 mm    -   Distance between the two last electrodes: 0.1 mm.    -   Initial beam size: 1 mm.

This snapshot (FIG. 15) of the simulation is taken before the ions reachthe exit electrode pair. Few ions are discharged on the first ringelectrode. The estimated resolution is 13 for the light ions and 18 forthe heavy ions. In FIG. 16, the conditions are the same as those of FIG.15, and the snapshot is taken when the ions have arrived. The overalltransmission is about 55%. Few ions are lost at the first ring but mostat the exit electrode pair. In comparison with the previous design, thedistance between two last pairs is limited to 0.5 mm to reduce the iondiffusion and beam divergence. For the same reason, the distance betweenexit electrodes is 100 μm. The resolving power is similar to theprevious case. Four ions out of initial 200 are lost discharged on theentrance electrode.

For a higher axial voltage (1800 V) along the cell (see FIG. 17 and FIG.18), the ion transmission is about 70%. Applying an RF-voltage betweenelectrodes does not improve the results. FIG. 17 has the same cellcharacteristics and simulation parameters as described in FIG. 16 exceptthat a higher overall axial voltage is applied (1800 V instead of 1200V). This higher field leads to a lower ion loss at the entranceelectrode. This snapshot is taken just before ions go through the lastelectrode pair and shows a highly focused beam. The estimated resolutionis then 17 for the light ions and 12 for the heavy ions. FIG. 18 also isthe same simulation as described in FIG. 17, at time of ion arrival atend of drift tube. The overall transmission is 71%. Ions are mainly lostat the exit electrode pair.

FIG. 19 and FIG. 20 show results for a 100 V RF-voltage. A noticeablenumber of small ions are decomposed at the end of the cell. Hence only73 out of the initial 200 ions exit the cell. The simulation of FIG. 19uses the same cell characteristics and simulation parameters asdescribed in FIG. 15 except that a 100 V-RF voltage is superimposed tothe DC axial voltage (1200 V). The snapshot of FIG. 19 is taken justbefore ions pass the last electrode pair. In contrast with whatsimulations for periodic field cells demonstrate, the addition of an RFfield does not improve the focus. The estimated resolution is 14 for thelight ions and 12 for the heavy ions. FIG. 20 shows the same simulationas that in FIG. 19; the snapshot being taken when the ions have arrivedat the end of the drift cell. The overall transmission is lower thanwithout RF (36% versus 55%).

-   -   2. SIMS

For the same cell as used in section 1.B. above (and a pressure of 10mTorr in the ion formation region, the transmission of the SIMS ions islower than that with a MALDI source; about 40% and 10% for ions havinginitial energy 0.1 eV (FIG. 21) and 1 eV (FIG. 22), respectively. Mostions are lost on the entrance electrode. Ions making through theentrance orifice are focused and transmitted through the first electrodeof the exit pair. Coating the entrance aperture with thin insulator orusing piezoelectric thin films, which themselves may be coated with athin insulator, can markedly improve this transmission against themobility gas counter-flow.

3. Testing of the Cell Prototype by Using Atmospheric Corona Dischargeand Direct Current Measurements.

The instrumental platform is shown in FIG. 23. Two modifications of thecell were tested. In the first one (FIG. 23A) a short (0.7″) cell waspumped from the back side through the wide (2.2 mm diameter) opening.The air pressure was maintained around 2 Torr. The vacuum insulation wasprovided by the use of O-rings (80) of different thickness, which alsoserved as variable spacers. The corona discharge created by applyinghigh voltage between the sharp wire tip (83) and the entrance electrode(87) served as an ion source. The electrodes were connected by aresistor chain (90) to provide necessary voltage drops. This setupallows estimation of the maximum voltages that can be applied betweenthe electrodes and across the entire cell, and estimation of the ionlosses on the electrodes.

The dimensions and spacing of the 4 pairs of electrodes were similar tothose of the simulation 1 b), but did not include a small aperture. Itwas possible to apply up to 600 V between individual electrodesseparated by only 0.6 mm, and the maximum total voltage was only limitedby the power supply capability. The transmission was measured at biasvoltages of up to 1700 V across the entire cell.

To estimate the divergence of the ion beam the current on the electrodeplaced immediately after the last cell ring was compared to the currententering the cell (all electrodes shorted). The current measurementsdemonstrate that practically no ions are lost on the intermediateelectrodes at 1700 V across the mobility cell, whereas when no voltageis applied the transmission is only about 20%, and it is probablydetermined by the efficiency of the ion transport in the gas flow fromthe region of high pressure towards the pumping port.

Using a two times longer (1.5″) cell in the same setup, a transmissionof more than 50% was detected. A more direct transmission measurementwas produced in the second modification of the instrumental platform(FIG. 23B), where an actual orifice (500 μm diameter) was introduced atthe end of the cell. To maintain the similar pressure regime, twoadditional peripheral openings (93) in the skimmer were made. All othercomponents are as indicated for FIG. 23A. The measurements revealed thatdue to the presence of these side holes, the gas flow at the skimmeraperture is perpendicular to the axis of the cell, and the ions areentrained towards the periphery. Thus, the transmission through theaperture went from 0.1% with no voltage applied to 6-7% at1700V—significantly less than in the case of no aperture. At the sametime, the ion current through the side openings does not change with thevoltage. These results suggest that in order to achieve hightransmission through the skimmer aperture, a divergent gas flow in thevicinity of the orifice must be avoided.

This condition is automatically fulfilled for the MALDI-IM experimentwhere the pressures in the sample region and in the cell are the same.When using the cell as a high pressure interface, additional measureshave to be taken in order to prevent the ion diffusion due to the flowof gas that is being differentially pumped.

The results of these preliminary tests show that the proposedconfiguration of electrodes allows one to apply significantly highervoltages compared to a periodic field cell with equally spacedelectrodes, and that the field configuration helps to confine the ionswithin a narrow region close to the cell separation axis.

4. Testing of the Cell in MALDI-IMS o-TOF Setup

Testing of the new mobility cell was performed in combination withcompact orthogonal time-of-flight mass spectrometer and a MALDI source.FIG. 24 shows the experimental setup with sample (97), mobility cell(100), and mass spectrometer (104). A test cell with the followingparameters was tested.

-   -   Electrode thickness: 0.625 mm    -   Distance between paired electrodes: 1.250 mm    -   Distance between pairs: 2.500 mm    -   Opening diameter: 3 mm    -   Skimmer orifice diameter: 0.500 mm    -   Number of electrodes: 56    -   Total cell length: 140 mm    -   Sample-cell distance: 4 mm

The cell was tested at a bias voltage of up to 1800V; the sample wasbiased up to 100V with respect to the cell entrance. The obtainedmobility resolution values (up to 40) were close to the ones predictedby simulations for these voltages and geometry.

Preliminary transmission measurements revealed a significant improvementcompared to the periodic cell design operated at the same bias voltage.Sensitivity test for the small (1040 a.m.u.) angiotensin II peptidemolecule demonstrated a detection limit of 2.5 femtomole. Experimentsinvolving different ratios of the electrical fields in small and largegaps demonstrates an optimum corresponding to a two times higher fieldin small gaps.

The effect of the placing of the mobility cell entrance close to thesample (at about 4 mm) and using conical electrode design, when comparedto the standard 1″ separation was found to result in an approximatelytwofold increase in total transmission.

The new design allows one to apply voltages that are impossible in aregular periodic or linear mobility cell due to the possibility of adischarge. At a certain level (typically about 2000 V), the mobilityresolution improvements become negligible while the collision induceddissociation of ions increases. The increase in the cell gas pressureallows avoidance of ion fragmentation at higher fields. However, therequirements for the high vacuum in the mass analyzer section limit thecell pressure to the range below 10 Torr. This pressure limitation canbe removed by using higher pumping speed in the mass spectrometer whichwould allow the mobility cell to be operated at even higher pressuresand voltages.

FIG. 25 shows a typical two-dimensional spectrum obtained using thedescribed instrumental arrangement. Mass/charge is plotted on the Xaxis, while mobility drift time is plotted on the Y axis. Signals from amixture containing peptides, dyes and C₆₀ are clearly visible. Themobility resolution is in the 30-40 range.

Because of its high transmission, small cross-section/length, highresolution, and the approximately 1-100 Torr operating pressure, thereare numerous applications where the new mobility cell is quite useful.One such application is the improvement of laser post ionizationsecondary neutral mass spectrometers. Such spectrometers rely onprocessing secondary ions and neutrals which are desorbed from a surfaceby an energetic particle source or by a photon beam. The m/z ratio ofthe desorbed secondary ions are determined by a mass spectrometer(usually a time of flight) and then the desorbed neutrals areionized—usually by a focused laser beam—and their m/z is then determinedin the same mass spectrometer. A particularly powerful laser desorptionmicroscope based on this principle is described by Pellin et al. in“TOF-SIMS: Surface Analysis by Mass Spectrometry” (IM Publications,Surrey U.K, 2002), chapter 14, page 375. This spectrometer first desorbsions by using either a microfocused liquid metal ion beam or a laserbeam which is microfocused by a Schwarzschild microscope to a sub microndiameter. The desorbed ions then travel away from the sample. After asuitable period of time (varying from a few hundred nanoseconds toseveral microseconds depending on the type or molecule or element to bedetected), a laser post ionization pulse is applied to a several cubicmm volume which can contain up 30% of the desorbed neutral atoms. Thesize of this volume must be as small as possible both to minimize thelaser power and to improve the mass spectral resolution of the time offlight. On the other hand, the volume must be as large as possible tocollect as many of the laser desorbed neutrals as possible. A solutionto this dilemma is the addition of an ion mobility cell within thecoaxial volume of the Schwarzschild microscope. At present, the designof Pellin uses this coaxial volume for the ion optics which arenecessary to transport desorbed ions from the sample into a three meterlong traditional coaxial reflector time-of-flight mass spectrometer.Even with the use of such a large spectrometer the achieved massresolution is only around 1000 from the large spatial volume containingthe post ionized neutrals.

In contrast, the addition of the new low profile IM-oTOFMS spectrometerdescribed herein (see FIG. 1) into the small coaxial ion transportvolume of the Schwarzschild optics solves these problems. One Torr ofhelium transport gas first injected onto the sample surface (2) servesto cool both the desorbed neutrals and ions. This cooling restricts thevolume into which they expand. The extraction field separates the ionsfrom the neutrals and the ions progress into the IM cell. Thepost-ionization laser (4) can then be used several microseconds afterthe initial desorption pulse (1) to intercept the neutral packet whichis being slowly drifted toward the mobility cell by the mobility carriergas flow. Helium carrier gas is transparent to wavelengths into the hardUV so the post-ionization process of the neutrals will not be impeded.The post-ionized neutrals are then transported into the mobility cellwhere they are resolved according to charge/volume. If there areidentical types of directly desorbed ions and post ionized neutral ionsfrom the sample then these identical ions formed from the two processeswill appear along parallel trend lines separated by a time equal to thedifference of the application of the primary desorption energy pulse (1)and the post-ionizing energy pulse (4). Because the desorption andionization events are decoupled from the mass analysis and because ofthe high transmission of the new mobility cell design, utilization ofhigher than 30% of all desorbed elements and molecules and a massresolution of 5,000 in a instrument whose physical size is {fraction(1/20)}^(th) the size of the existing laser post-ionizationspectrometers can be achieved.

Interfacing with the Time-of-Flight Mass Spectrometer

The TOF mass spectrometer requires high vacuum conditions to operate.Therefore, additional measures may be required to make a transition frompressures typical for the mobility cell (1-5 Torr) to the TOF MS section(10⁻⁶-10⁻⁷ Torr). These include the use of small orifices anddifferentially pumped interfaces. FIG. 26A demonstrates the combinationof a special mobility interface tube with the differential pumpingincluding a conical skimmer. In this figure, there is a sampleintroduction (108) at the entrance of the mobility cell (112). Uponexiting the mobility cell (112), ions enter a differential pumpinginterface (124) through an orifice (116) located between an interfacedrift tube (120) and the mobility cell (112). Additional focusing toimprove throughput is accomplished by the use of the interface drifttube (120). This is followed by a skimmer cone (128) and extractor andbeam forming optics (132) which prepare the analyte species for entryinto another analytical platform, preferably a time-of-flight massspectrometer. FIG. 26B is an expanded view of the interface drift tube(120). The mass spectrometer can ideally be one of the configurationsusing a position sensitive detector as described in the following: U.S.Pat. No. 6,683,299 to Fuhrer et al.; in copending application Ser. No.10/155,291 to Fuhrer et al. filed on Oct. 20, 2003; and in the U.S.application of Fuhrer et al. filed on Oct. 18, 2003 and having attorneydocket Ser. No. ______ HO-P02142US3 (application number not yetassigned). which includes the ability to read and keep separate the ionoutput of multiple IMS channels using only one mass spectrometer.

The use of an extra drift tube placed right after the main mobility cellis based on the necessity to provide a smoother pressure drop after theskimmer orifice, and to form a high quality molecular beam with lowdivergence and ion energy spread. In a preferred embodiment, these twoparameters achieve high resolution and sensitivity of the massspectrometer. The channel diameter in the interface is larger than thatof the mobility cell, and the applied field is lower due to lowerpressure. The focusing of ions is achieved using the same method as inthe main mobility—by varying the distances between electrodes. If thevoltage applied to the gaps between the electrodes is the same, thefield is stronger in the small gaps, and there is a field penetrationinto the large gaps, which produces the focusing effect.

Simulations show that it is possible to achieve the divergence of lessthan 0.08 rad, and the energy spread of 0.4-0.6 eV. The theoreticaltransmission of 100% can be achieved with specific voltage settings. Atthe end of the channel, the pressure is about one order of magnitudelower than in the mobility cell. The next region is evacuated by highspeed pumping in order to further reduce the flow of the carrier gasinto the TOF. This allows achieving high vacuum conditions in the massspectrometer as well. Experimental data shows that efficient pumping inthis region can achieve the theoretical levels of resolution andtransmission of the mobility setup. The pumping also has to besymmetrical in order to avoid preferential side flow of the gas from theorifice which can entrain the ions away from the skimmer. This effectcan occur at relatively low pressures and produce further signal losses.

The gas molecules may be skimmed using a conical shape skimmer (orskimmers of different shapes as well). The pressure in the region behindthe skimmer is already very low so that ions can be efficientlyextracted using only slightly biased TOF primary beam optics.

The effect of using an additional mobility interface section (see FIG.26) after the main cell has been tested. The experimental data showsthat there is no or very little ion loss in the interface. The mobilityresolution after the interface is only about 10% lower than theresolution right after the mobility cell. The pressure drop in theinterface allowed operating at 2.5× higher pressure and applying 2×higher voltage across the mobility cell. This achieves high resolutionusing a very short (5″) drift cell.

Another configuration suggested by the superior performance propertiesof the IM-oTOFMS is for laser ablation of aerosol particles or forfragmentation or photoionization of mobility separated ions. It ispossible to produce such particles comprising MALDI matrix and analyteor also analyte and small light adsorbing particles which can act as aMALDI substrate for large bio-ions. Such particles can be ionized andtransported with a mobility cell or they may alternatively remainneutral and be transported by a flow tub. FIG. 27 schematicallyillustrates the use of a mobility cell or some other gas transportdevice (158) to inject ionized or non-ionized particles or molecules(156), i.e., neutral species, into the entrance region between twoopposing IM-oTOFMS spectrometers (148 and 152), the region between thetwo opposing IM-oTOFMS comprising two opposing mobility cells (140) and(144). The two mobility drift cells are configured in a substantiallyhorizontally opposed manner, i.e., having separation axes configured180° or approximately 180° from one another. In the entrance region, theion or neutral species may be subjected to a fragmentation source. Oneof the oTOFMS operates in negative mode, while the other operates inpositive mode. After the analyte (156) is injected into this region, itis irradiated with ionizing radiation (160). Both positive and negativeions are created and are transported by the opposing fields into one orthe other of the appropriately biased spectrometers. The bias of theentrance to the spectrometers can be controlled by a computer sequenceso that the region between the entrance to the mobility cells is fieldfree. Analyte (156) can then drift (either as ions or as neutrals) alongwith the gas flow which is orthogonal to the axis of the mobility cells.At an appropriate time extraction pulses are simultaneously orsequentially applied to the face of the mobility cells so that ions areextracted into the respective mobility cells according to the ionpolarity. At some time later, ionizing radiation can be applied toconvert the gas transported neutrals into ions and these post ionizedneutrals would also enter the two mobility cells. All of thepost-ionization features described previously as referenced to FIG. 1would apply for both the negative and positive mobility spectrometers.Although FIG. 1 and FIG. 27 illustrate a single channel of mobility ineach polarity IMS, it is understood that the mobility cells can also bemulti-channeled mobility cells as described in this application and inthe following: U.S. Pat. No. 6,683,299 to Fuhrer et al.; in copendingapplication Ser. No. 10/155,291 to Fuhrer et al. filed on Oct. 20, 2003;and in the U.S. application of Fuhrer et al. filed on Oct. 18, 2003 andhaving attorney docket Ser. No. ______ HO-P02142US3 (application numbernot yet assigned). All of the aforementioned patents and patentapplications are incorporated by reference as though fully describedherein. Thus there is an instrument which allows high mass and mobilityresolution of simultaneously laser-desorbed ions and post-ionizedlaser-desorbed neutrals. This configuration is obviously not restrictedto the analysis of aerosol particles. For example the entraining of ionsand neutrals desorbed from a surface as described already in paragraph[112] can be accomplished so that the gas stream is directed between thetwo mobility cells. This is particularly useful for microprobe imagingof a surface and allows the time width of the desorbing radiation whichimpinges a surface to be comparable to the drift time of the entraininggas flow which can be many 10's of microseconds depending on gaspressures and flow conditions. This approach is particularly effectivewhen the two mobility cells have multiple channels allowing collectionof ions from a several cm long gas flow between the two opposingmobility cells.

Addition of Repulsively Biased Conical Electrode to Improve Focusing ofIons Through Multiaperture Double Electrode Structures

FIG. 6C illustrates the addition of a third biasable element which ismade of electrically connected small cones which are positioned abovethe solid “web” region between the multiapertures. Thus each compositemobility electrode structure comprises three biasable elements separatedby thin insulator layers. An example is shown from a simulation in which10 eV positive ions of mass 720 are drifted through 2 Torr of heliumtoward the composite multiaperture mobility electrode. The conicalelectrode element is biased as indicated to a +8.3 eV repulsivepotential which serves to repel the ions away from the “web” regionwhere they would otherwise collide and be lost if the conical structurewere not there. The ions are deflected by the combination of this fieldand by the gas flow into the apertures. The deflected ions are thentransmitted by the attractive potential provided by the two electrodecouplet which provide field penetration from the back electrode into thecenter of the aperture. All biases would be reversed for the purpose oftransmitting negative ions.

It should be understood that this conical biasable element can be addedto any of the multi-aperture structures previously described and thusimprove transmission through these devices. Although the conicalstructure may be made of any conductor or semiconductor, it may alsocomprise an insulator thin film. This insulator thin film wouldinitially charge as the first few ions come through the mobility celland thereafter would serve to repel subsequent ions through themulti-apertures. An alternative structure would have the conicalstructure fabricated from thin film piezoelectric structures (whichthemselves could be coated with a thin dielectric film) which could bebiased to produce a surface dipole which would act to repel approachingions.

Another embodiment would make each electrode from flexible circuit boardcopper-kapton-copper material. Desired hole arrays would either bepunched or laser drilled into a cut coupon of the material so that theelectrical isolation of the front and back copper was maintained.Electrical connection to the front and back isolated copper electrodescould be formed by known circuit board etching techniques. The couponscould then be aligned and sandwiched together in a mechanical jig andmold into which epoxy would be poured and cured. The high vacuum epoxywould make a suitable vacuum seal and the intimate electrical contact ofthe back of one coupon to the face of the next would eliminate any ofthe exposed web areas and would thus form small individual ion mobilitycolumns each of which could be used to resolve its own stream of ions.The electrical biasing of each element would be easily done by acombination of power supplies and resistors applied to the leads whichwould emerge from the hardened epoxy housing. The interface region (120)of FIGS. (26A and 26B) can also be made by this technique. The interfaceregion (120) can also be located outside of the vacuum housingcontaining the skimmer and differential pumping capability.

An ideal multibore IMS cell would feed each of its channels directlyinto a multihole skimmer and thence into the oTOFMS or it could also befed through an RF mulitpole cooling apparatus as shown in FIG. 28 whichserves to keep the output of each channel spatially separated andsubstantially parallel as each goes into an ion detection device whichmay be a oTOFMS equipped with a position sensitive detector.

Multi-Channel Ion Interface

Another embodiment of the invention, illustrated in FIGS. 28A and 28B,combines a multi-channel RF interface between the exit of themulti-channel mobility cell (165) and the input to the extraction regionof the MS (170). Between the mobility cell (165) and the MS (170) is amulti-stage RF focusing interface (components (175) and (180) in theexample of the drawings illustrating two stages). Ions (190) exit themobility cell (165) and enter the RF interface region. In FIG. 28B, across-sectional view of the second RF region (180 from FIG. 28A; alsoreferred to as section A-A)) is shown. The multiple ion beamlets whichemerge from the multiple channels of the IM cell and interface assemblycan be directed through one or more stages of gas filled RF multipoleion guide. FIG. 28B shows eight separate ion beamlets (one of which islabeled as (200) traversing the section RF stage shown in cross-section.Each beamlet is directed into its own two stages of an RF multi-polemulti-channel ion guide assembly. The number of optical elements chosenin FIG. 28 is arbitrary and one skilled in the art will realize thatmany additional elements can be added to a typically sized TOFinstrument. The assembly has a rectangular envelope (195) and sixteenrods (205) located as shown in the cross-sectional view of FIG. 28B. InFIG. 28 each of the two rectangular envelopes (one for each RF stage inFIG. 28) and the sixteen rods in each stage are electrically connectedto a common DC potential and so have the same DC potential foracceleration of ions coming into each stage. The rods additionally aresupplied by RF-voltages of opposite phases and the same amplitude (+Usin ωt and −U sin ωt). Ions are focused to positions around the pointsof zero RF-field.

A particularly useful and powerful embodiment of this device is for thecase when ions have been separated on the basis of their charge tovolume ratio by an IMS cell prior to their entering the RF interface. Inthis case the amplitude or frequency of the RF field can be continuouslyoptimized to maximize the transmission of the particular charge tovolume ratio which is present at any particular time relative to thestart of the IMS separation. This is very useful for MALDI-IMSexperiments in which the singly ionized charge state is predominant. IMSof familial classes of biomolecules have been found to have apredictable relationship between the charge to volume and the charge tomass of each ion in the familial class. This relationship is differentfor most familial classes of singly charge biomolecular ions (e.g.,lipids, peptides, oligonucleotides) so that each ion of a familial classlies along a distinct familial “trend line” in the two dimensional plotof mobility drift time vs. m/z. Thus, the time of arrival of an ion witha particular m/z can be predicted by the familial trend line and themobility drift time (which is related to the ion's volume to chargeratio) so the RF amplitude, or frequency can be continuously computercontrolled and optimized for the transmission of the specific m/z ofeach ion in the familial trend line. Thus, the RF field would haveoptimal characteristics for low m/z values at the start of the IMseparation and very different field characteristics as the larger m/zions eluted from the IM cell at longer mobility drift times. Anapproximately linear increase of m/z values along a familial trend lineoccurs. It is a reasonable approximation to increase the amplitude ofthe RF-voltage which is applied to the rods to be proportional to thesquare root of the time measured relative to a zero time when theinitiation of the ionization event occurs. The coefficient ofproportionality is the slope of the familial trend line. Such a timechanging RF-field thus synchronized to the elution of ions at the end ofthe mobility cell would allow to record small ions without defocusingand losing them due to possible instability of their motion for largeRF-fields necessary for the focusing and transport of larger ions. Alsoit would allow the effective focusing of ions of large masses foressentially the same width ion beams for ions of all masses. Sincemulti-charged ions would be focused even better than for the singlycharged ions such an approach will focus all ions well below 1 mmdiameter ion beams as the corresponding simulations show. The length andthe number of the sections and the DC voltages applied to them should befound by computer simulation for providing enough time for desired ionfocusing without losing of their separation received before in mobilitycell and without decomposing of the ions. Any broadening of the mobilityresolution because of the increased residence time of ions in the RFassembly could be almost completely removed by numerical deconvolutionof the mobility resolved spectra after first determining—eitherexperimentally or theoretically—the residence time as a function of massof the ions within the RF assembly.

An RF-field ion focusing gives ions additional energy of ion motion inthe plane orthogonal to axis being equal to the ion thermal energy. See,for example, Raznikov, et al RCM V 15, 1912-1921 (2001). If the axialvelocity of ions is small in comparison with average thermal velocity ofhelium (˜1300 m/sec) then the thermal energy of ions corresponds to theroom temperature and it is about 0.013 eV per 1 degree of freedom. Ofinterest here is the degree of freedom which lies in the plane of thechannels of our ion guide orthogonal to the direction of ion motionwhich due to RF-field contribution wherein we would have about 0.026 eVenergy. For the energy of ion motion in the axial direction 26 eV whichis typical for ions coming into the TOF MS then the divergence angle onaverage would be about 0.03 rad. The ion beams would, on average, be 6mm wide after traveling 10 cm. The distance between ion beams of 6 mmand the width of recording plate 50 mm would be enough for recording theoutput of eight individual channels.

Although the present invention and its advantages have been described indetail, it should be understood that various changes, substitutions andalterations can be made herein without departing from the invention asdefined by the appended claims. Moreover, the scope of the presentapplication is not intended to be limited to the particular embodimentsof the process, machine, manufacture, composition of matter, means,methods and steps described in the specification. As one will readilyappreciate from the disclosure, processes, machines, manufacture,compositions of matter, means, methods, or steps, presently existing orlater to be developed that perform substantially the same function orachieve substantially the same result as the corresponding embodimentsdescribed herein may be utilized. Accordingly, the appended claims areintended to include within their scope such processes, machines,manufacture, compositions of matter, means, methods, or steps.

1. An apparatus comprising: an ion source, a first ion mobility driftcell, said first ion mobility drift cell having an entrance fluidlycoupled to the ion source, said first ion mobility drift cell comprisingat least two electrode pairs having an intra-electrode gap betweenindividual electrodes of a pair which is smaller than an inter-electrodegap between electrode pairs, and an exit.
 2. The apparatus of claim 1,wherein electrodes near the exit of the ion mobility cell have greaterthickness than electrodes further removed from the exit of the ionmobility cell.
 3. The apparatus of claim 1, wherein the electrodes nearthe exit of the ion mobility cell are of smaller diameter thanelectrodes further removed from the exit of the ion mobility cell. 4.The apparatus of claim 1, wherein the electrodes near the exit of theion mobility drift cell have one or more apertures comparable indimension to the dimensions of the exit.
 5. The apparatus of claim 1,wherein one or more electrode pairs near the entrance of the ionmobility cell have smaller outside diameter than one or more electrodepairs farther away from the entrance.
 6. The apparatus of claim 5,wherein the first several sets of electrodes near the entrance of theion mobility cell have an increasing outside diameter in the directionof said exit.
 7. The apparatus of claim 1, further comprising an RFvoltage and a dc electrode voltage, wherein said RF voltage issuperimposed on said dc electrode voltage.
 8. The apparatus of claim 1,further comprising a time-of-flight mass spectrometer fluidly coupled tothe exit of the mobility drift cell by way of an orthogonal extractorand a low energy monochromatized electron beam coupled to saidorthogonal extractor.
 9. The apparatus of claim 1, wherein the exitcomprises a plurality of apertures.
 10. The apparatus of claim 9,wherein the plurality of apertures is comprised of a 4033 circular arrayof apertures, the array having a diameter of 5.37 mm and a totalaperture area of 8 mm².
 11. The apparatus of claim 1, wherein one ormore electrodes in the drift cell has a plurality of apertures.
 12. Theapparatus of claim 11, wherein the distribution of apertures in theelectrodes changes from said entrance to said exit.
 13. The apparatus ofclaim 12, wherein the distribution of apertures changes from a circulardistribution to a horizontal rectangle distribution.
 14. The apparatusof claim 1, wherein the exit is at least partially coated with a thininsulating film.
 15. The apparatus of claim 14, wherein the insulatingfilm comprises piezoelectric film.
 16. The apparatus of claim 1, whereinone or more electrodes comprise piezoelectric thin films.
 17. Theapparatus of claim 1, wherein said first mobility drift cell has one ormore collision induced dissociation regions within it.
 18. The apparatusof claim 17, wherein the collision induced dissociation region is placednear the exit of said mobility drift cell.
 19. The apparatus of claim17, wherein the collision induced dissociation region is placed near thecenter of said mobility drift cell.
 20. The apparatus of claim 1,wherein the ion mobility drift cell further comprises at least oneporous semiconductor electrode.
 21. The apparatus of claim 20, wheresaid at least one porous semiconductor electrode is located directlyafter the entrance.
 22. The apparatus of claim 20, wherein said at leastone porous semiconductor electrode is coated with a dielectric orpiezoelectric thin film.
 23. The apparatus of claim 1, where said ionsource is a MALDI source.
 24. The apparatus of claim 1, where said ionsource is a secondary ion source.
 25. The apparatus of claim 1, whereinone or more of said electrode pairs are replaced with electrodes triads.26. The apparatus of claim 1, wherein at least one of said electrodes isa multiaperture conical skimmer electrode.
 27. The apparatus of claim 1,further comprising a differentially pumped interface fluidly coupled tosaid ion mobility drift cell; a conical skimmer fluidly coupled to saiddifferentially pumped interface; an extractor fluidly coupled to saidconical skimmer; and, a time-of-flight mass spectrometer fluidly coupledto said extractor.
 28. The apparatus of claim 1, further comprising adifferentially pumped interface fluidly coupled to said ion mobilitydrift cell; a multihole skimmer fluidly coupled to said differentiallypumped interface; an extractor fluidly coupled to said multiholeskimmer; and, a time-of-flight mass spectrometer fluidly coupled to saidextractor.
 29. The apparatus of claim 1, wherein said ion mobility driftcell forms part of a multibore ion mobility spectrometer.
 30. Theapparatus of claim 1, wherein at least one of said electrode pairs iscomprised of flexible copper-kapton-copper material.
 31. The apparatusof claim 1, further comprising a multichannel RF interface fluidlycoupled to said drift cell; an extractor fluidly coupled to saidmultichannel RF interface; and, a time-of flight mass spectrometerfluidly coupled to said extractor.
 32. The apparatus of claim 1, furthercomprising: an second ion mobility drift cell fluidly coupled to saidfirst ion mobility drift cell, said second ion mobility drift cellcomprising electrode pairs having an intra-electrode gap which issmaller than an inter-electrode gap between electrode pairs; and, adifferentially pumped interface fluidly coupled to said second ionmobility drift cell.
 33. The apparatus of claim 32, further comprising aconical skimmer fluidly coupled to said differentially pumped interface;an extractor fluidly coupled to said conical skimmer; and, atime-of-flight mass spectrometer fluidly coupled to said extractor. 34.The apparatus of claim 32, wherein one or more of said electrode pairsof said first ion mobility drift cell, said second ion mobility driftcell, or both, are replaced with electrodes triads.
 35. An apparatuscomprising: a source of ion or neutral species, a first and second ionmobility drift cell, said first and second ion mobility drift cellsbeing substantially horizontally opposed to one another and fluidlycoupled to said source, wherein one or both of said ion mobility driftcells comprise at least two electrode pairs having an intra-electrodegap between individual electrodes of a pair which is smaller than aninter-electrode gap between electrode pairs, and, a first massspectrometer fluidly coupled to said first ion mobility drift cell and asecond mass spectrometer fluidly coupled to said second ion mobilitydrift cell.
 36. The apparatus of claim 35 further comprising afragmentation source positioned to fragment ions and neutral speciesentering one or both of said first and second ion mobility drift cells.37. The apparatus of claim 35 where said first mass spectrometer, saidsecond mass spectrometer, or both, are time-of-flight massspectrometers.
 38. A method of analyzing ions according to theirmobility in a gas comprising: a first ionization step to form ions froman analytical sample, introducing said ions into a mobility drift cell,applying regions of alternating high and low electric field along theseparation axis of the drift cell, and detecting the ions.
 39. Themethod of claim 38, further comprising the step of applying an RFvoltage superimposed on a dc electrode voltage along at least a part ofsaid separation axis.
 40. The method of claim 38, further comprising thestep of changing the charge of ions after said step of applying.
 41. Themethod of claim 38, wherein said step of detecting comprises detectingwith a mass spectrometer.
 42. The method of claim 41, wherein said massspectrometer is a time-of-flight mass spectrometer.
 43. The method ofclaim 42, further comprising the step of RF focusing of said ions beforesaid step of detecting with a time-of-flight mass spectrometer.
 44. Themethod of claim 38, wherein the step of said first ionization comprisesforming ions using a MALDI ion source.
 45. The method of claim 38,wherein the step of said first ionization comprises forming ions using asecondary ion source.
 46. The method of claim 38, wherein the step ofsaid first ionization comprises forming ions using a electrosprayionization combined with an ion trap.
 47. The method of claim 38,further comprising a second ionization step.
 48. The method of claim 38,wherein said step of applying regions of alternating high and lowelectric field comprises applying two substantially horizontally opposedregions of alternating high and low electric field through the use oftwo substantially horizontally opposed ion mobility drift cells.
 49. Themethod of claim 48, wherein said step of detecting comprises detectingwith a mass spectrometer.
 50. The method of claim 49 wherein said stepof detecting with a mass spectrometer comprises detecting with atime-of-flight mass spectrometer.